#include "mode.h"
#include "ichisize.h"
#include "util.h"

Include dependency graph for extr_ct.h:

This graph shows which files directly or indirectly include this file:

Data Structures
struct	AtData

struct	tagStereoCarb

struct	tagStereoDble

struct	tagIsotopicAtom

struct	tagAtom

Macros
#define	NUM_CHEM_ELEMENTS 127 /* well above number of known chem. elements */

#define	AT_ISO_SORT_KEY_MULT 32 /* up to 32 identical hydrogen isotopes */

#define	BYTE_BITS 8 /* number of bits in one byte */

#define	BOND_MASK 0xf /* 4 bits */

#define	BOND_BITS 4 /* 3 or 4 does not matter; 2 is too small for BOND_TAUTOM */

#define	BOND_ADD (BOND_BITS==2?-1:0) /* subtract 1 from bonds stored in CT */

#define	BOND_SINGLE BOND_TYPE_SINGLE /* 1 */

#define	BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */

#define	BOND_TRIPLE BOND_TYPE_TRIPLE /* 3 */

#define	BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */

#define	BOND_ALT_123 5 /* single/double/triple */

#define	BOND_ALT_13 6 /* single/triple */

#define	BOND_ALT_23 7 /* double/triple */

#define	BOND_TAUTOM 8

#define	BOND_ALT12NS 9

#define	BOND_NUMDIF 9 /* number of different kinds of bonds */

#define	BOND_TYPE_MASK 0x0f

#define	BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */

#define	BOND_MARK_ALT12 0x10

#define	BOND_MARK_ALT123 0x20

#define	BOND_MARK_ALT13 0x30

#define	BOND_MARK_ALT23 0x40

#define	BOND_MARK_ALT12NS 0x50 /* 1 or 2, non-stereo */

#define	BOND_MARK_MASK 0x70

#define	ACTUAL_ORDER(PBNS, IAT, IBOND, BTYPE)

#define	BITS_PARITY 0x07 /* mask to retrieve half-bond parity */

#define	MASK_CUMULENE_LEN 0x38 /* mask to retrieve (cumulene chain length - 1)MULT_STEREOBOND /

#define	KNOWN_PARITIES_EQL 0x40 /* parity is same for all pairs of constit. equivalent atoms */

#define	MAX_CUMULENE_LEN 2 /* max number of bonds in a cumulene chain - 1 */

#define	MULT_STEREOBOND

#define	MAKE_BITS_CUMULENE_LEN(X) ((X)*MULT_STEREOBOND)

#define	GET_BITS_CUMULENE_LEN(X) ((X)&MASK_CUMULENE_LEN)

#define	BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/

#define	IS_ALLENE_CHAIN(X) ((GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND)%2)

#define	AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */

#define	AB_PARITY_ODD 1 /* 1 => odd parity */

#define	AB_PARITY_EVEN 2 /* 2 => even parity */

#define	AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */

#define	AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */

#define	AB_PARITY_IISO 5 /* 5 => no parity because of identical atoms */

#define	AB_PARITY_CALC 6 /* 6 => calculate parity later */

#define	AB_PARITY_0D 8 /* 8 => bit signifies 0D case -- not used */

#define	AB_INV_PARITY_BITS (AB_PARITY_ODD ^ AB_PARITY_EVEN)

#define	AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */

#define	AB_MIN_KNOWN_PARITY 1

#define	AB_MAX_PART_DEFINED_PARITY 3 /* 1, 2, 3 => defined parities, uncluding 'unknown' */

#define	AB_MIN_PART_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN, AB_PARITY_UNKN) */

#define	AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */

#define	AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */

#define	AB_MIN_ILL_DEFINED_PARITY 3

#define	AB_MAX_ILL_DEFINED_PARITY 4

#define	AB_MAX_ANY_PARITY 4

#define	AB_MIN_ANY_PARITY 1

#define	AMBIGUOUS_STEREO 1

#define	AMBIGUOUS_STEREO_ATOM 2

#define	AMBIGUOUS_STEREO_BOND 4

#define	AMBIGUOUS_STEREO_ATOM_ISO 8

#define	AMBIGUOUS_STEREO_BOND_ISO 16

#define	AMBIGUOUS_STEREO_ERROR 32

#define	MIN_DOT_PROD 50 /* min value of at->stereo_bond_z_prod[i] to define parity */

#define	ATOM_PARITY_VAL(X) (X)

#define	ATOM_PARITY_PART_DEF(X) (AB_MIN_PART_DEFINED_PARITY <= (X) && (X) <= AB_MAX_PART_DEFINED_PARITY)

#define	ATOM_PARITY_ILL_DEF(X) (AB_MIN_ILL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_ILL_DEFINED_PARITY)

#define	ATOM_PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= (X) && (X) <= AB_MAX_KNOWN_PARITY)

#define	ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY)

#define	ATOM_PARITY_NOT_UNKN(X) (ATOM_PARITY_KNOWN(X) && (X) != AB_PARITY_UNKN)

#define	PARITY_VAL(X) ((X) & BITS_PARITY)

#define	PARITY_PART_DEF(X) (AB_MIN_PART_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_PART_DEFINED_PARITY)

#define	PARITY_ILL_DEF(X) (AB_MIN_ILL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_ILL_DEFINED_PARITY)

#define	PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY)

#define	PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY)

#define	PARITY_CALCULATE(X) (AB_PARITY_CALC == PARITY_VAL(X))

#define	BOND_PARITY_PART_DEFINED(X) (PARITY_PART_DEF(X) \|\| PARITY_CALCULATE(X))

#define	BOND_PARITY_PART_KNOWN(X) (PARITY_KNOWN(X) \|\| PARITY_CALCULATE(X))

#define	ALL_BUT_PARITY(X) ((X)&~BITS_PARITY)

#define	ALWAYS_SET_STEREO_PARITY 0

#define	NO_ISOLATED_NON_6RING_AROM_BOND 0 /* for Yuri */

#define	SAVE_6_AROM_CENTERS 0 /* for Yuri */

Typedefs
typedef long	AT_ISO_SORT_KEY

typedef struct tagStereoCarb	AT_STEREO_CARB

typedef struct tagStereoDble	AT_STEREO_DBLE

typedef struct tagIsotopicAtom	AT_ISOTOPIC

typedef AT_NUMB	AT_STEREO

typedef struct tagAtom	sp_ATOM

Macro Definition Documentation

◆ AB_INV_PARITY_BITS

#define AB_INV_PARITY_BITS (AB_PARITY_ODD ^ AB_PARITY_EVEN)

◆ AB_MAX_ANY_PARITY

#define AB_MAX_ANY_PARITY 4

◆ AB_MAX_ILL_DEFINED_PARITY

#define AB_MAX_ILL_DEFINED_PARITY 4

◆ AB_MAX_KNOWN_PARITY

#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */

◆ AB_MAX_PART_DEFINED_PARITY

#define AB_MAX_PART_DEFINED_PARITY 3 /* 1, 2, 3 => defined parities, uncluding 'unknown' */

◆ AB_MAX_WELL_DEFINED_PARITY

#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */

◆ AB_MIN_ANY_PARITY

#define AB_MIN_ANY_PARITY 1

◆ AB_MIN_ILL_DEFINED_PARITY

#define AB_MIN_ILL_DEFINED_PARITY 3

◆ AB_MIN_KNOWN_PARITY

#define AB_MIN_KNOWN_PARITY 1

◆ AB_MIN_PART_DEFINED_PARITY

#define AB_MIN_PART_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN, AB_PARITY_UNKN) */

◆ AB_MIN_WELL_DEFINED_PARITY

#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */

◆ AB_PARITY_0D

#define AB_PARITY_0D 8 /* 8 => bit signifies 0D case -- not used */

◆ AB_PARITY_CALC

#define AB_PARITY_CALC 6 /* 6 => calculate parity later */

◆ AB_PARITY_EVEN

#define AB_PARITY_EVEN 2 /* 2 => even parity */

◆ AB_PARITY_IISO

#define AB_PARITY_IISO 5 /* 5 => no parity because of identical atoms */

◆ AB_PARITY_NONE

#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */

◆ AB_PARITY_ODD

#define AB_PARITY_ODD 1 /* 1 => odd parity */

◆ AB_PARITY_UNDF

#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */

◆ AB_PARITY_UNKN

#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */

◆ ACTUAL_ORDER

#define ACTUAL_ORDER	(	PBNS,
		IAT,
		IBOND,
		BTYPE
	)

Value:

( ((PBNS) && (PBNS)->edge && (PBNS)->vert &&\

((BTYPE)==BOND_ALT_123 || (BTYPE)==BOND_ALT_13 || (BTYPE)==BOND_ALT_23))? (PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].flow+BOND_TYPE_SINGLE:(BTYPE))

BOND_ALT_23

#define BOND_ALT_23

Definition extr_ct.h:219

BOND_ALT_13

#define BOND_ALT_13

Definition extr_ct.h:218

BOND_ALT_123

#define BOND_ALT_123

Definition extr_ct.h:217

BOND_TYPE_SINGLE

#define BOND_TYPE_SINGLE

Definition incomdef.h:67

◆ ALL_BUT_PARITY

#define ALL_BUT_PARITY ( X ) ((X)&~BITS_PARITY)

◆ ALWAYS_SET_STEREO_PARITY

#define ALWAYS_SET_STEREO_PARITY 0

◆ AMBIGUOUS_STEREO

#define AMBIGUOUS_STEREO 1

◆ AMBIGUOUS_STEREO_ATOM

#define AMBIGUOUS_STEREO_ATOM 2

◆ AMBIGUOUS_STEREO_ATOM_ISO

#define AMBIGUOUS_STEREO_ATOM_ISO 8

◆ AMBIGUOUS_STEREO_BOND

#define AMBIGUOUS_STEREO_BOND 4

◆ AMBIGUOUS_STEREO_BOND_ISO

#define AMBIGUOUS_STEREO_BOND_ISO 16

◆ AMBIGUOUS_STEREO_ERROR

#define AMBIGUOUS_STEREO_ERROR 32

◆ AT_ISO_SORT_KEY_MULT

#define AT_ISO_SORT_KEY_MULT 32 /* up to 32 identical hydrogen isotopes */

◆ ATOM_PARITY_ILL_DEF

#define ATOM_PARITY_ILL_DEF ( X ) (AB_MIN_ILL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_ILL_DEFINED_PARITY)

◆ ATOM_PARITY_KNOWN

#define ATOM_PARITY_KNOWN ( X ) (AB_MIN_KNOWN_PARITY <= (X) && (X) <= AB_MAX_KNOWN_PARITY)

◆ ATOM_PARITY_NOT_UNKN

#define ATOM_PARITY_NOT_UNKN ( X ) (ATOM_PARITY_KNOWN(X) && (X) != AB_PARITY_UNKN)

◆ ATOM_PARITY_PART_DEF

#define ATOM_PARITY_PART_DEF ( X ) (AB_MIN_PART_DEFINED_PARITY <= (X) && (X) <= AB_MAX_PART_DEFINED_PARITY)

◆ ATOM_PARITY_VAL

#define ATOM_PARITY_VAL ( X ) (X)

◆ ATOM_PARITY_WELL_DEF

#define ATOM_PARITY_WELL_DEF ( X ) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY)

◆ BITS_PARITY

#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */

◆ BOND_ADD

#define BOND_ADD (BOND_BITS==2?-1:0) /* subtract 1 from bonds stored in CT */

◆ BOND_ALT12NS

#define BOND_ALT12NS 9

◆ BOND_ALT_123

#define BOND_ALT_123 5 /* single/double/triple */

◆ BOND_ALT_13

#define BOND_ALT_13 6 /* single/triple */

◆ BOND_ALT_23

#define BOND_ALT_23 7 /* double/triple */

◆ BOND_ALTERN

#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */

◆ BOND_BITS

#define BOND_BITS 4 /* 3 or 4 does not matter; 2 is too small for BOND_TAUTOM */

◆ BOND_CHAIN_LEN

#define BOND_CHAIN_LEN ( X ) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/

◆ BOND_DOUBLE

#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */

◆ BOND_MARK_ALL

#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */

◆ BOND_MARK_ALT12

#define BOND_MARK_ALT12 0x10

◆ BOND_MARK_ALT123

#define BOND_MARK_ALT123 0x20

◆ BOND_MARK_ALT12NS

#define BOND_MARK_ALT12NS 0x50 /* 1 or 2, non-stereo */

◆ BOND_MARK_ALT13

#define BOND_MARK_ALT13 0x30

◆ BOND_MARK_ALT23

#define BOND_MARK_ALT23 0x40

◆ BOND_MARK_MASK

#define BOND_MARK_MASK 0x70

◆ BOND_MASK

#define BOND_MASK 0xf /* 4 bits */

◆ BOND_NUMDIF

#define BOND_NUMDIF 9 /* number of different kinds of bonds */

◆ BOND_PARITY_PART_DEFINED

#define BOND_PARITY_PART_DEFINED ( X ) (PARITY_PART_DEF(X) || PARITY_CALCULATE(X))

◆ BOND_PARITY_PART_KNOWN

#define BOND_PARITY_PART_KNOWN ( X ) (PARITY_KNOWN(X) || PARITY_CALCULATE(X))

◆ BOND_SINGLE

#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */

◆ BOND_TAUTOM

#define BOND_TAUTOM 8

◆ BOND_TRIPLE

#define BOND_TRIPLE BOND_TYPE_TRIPLE /* 3 */

◆ BOND_TYPE_MASK

#define BOND_TYPE_MASK 0x0f

◆ BYTE_BITS

#define BYTE_BITS 8 /* number of bits in one byte */

◆ GET_BITS_CUMULENE_LEN

#define GET_BITS_CUMULENE_LEN ( X ) ((X)&MASK_CUMULENE_LEN)

◆ IS_ALLENE_CHAIN

#define IS_ALLENE_CHAIN ( X ) ((GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND)%2)

◆ KNOWN_PARITIES_EQL

#define KNOWN_PARITIES_EQL 0x40 /* parity is same for all pairs of constit. equivalent atoms */

◆ MAKE_BITS_CUMULENE_LEN

#define MAKE_BITS_CUMULENE_LEN ( X ) ((X)*MULT_STEREOBOND)

◆ MASK_CUMULENE_LEN

#define MASK_CUMULENE_LEN 0x38 /* mask to retrieve (cumulene chain length - 1)*MULT_STEREOBOND */

◆ MAX_CUMULENE_LEN

#define MAX_CUMULENE_LEN 2 /* max number of bonds in a cumulene chain - 1 */

◆ MIN_DOT_PROD

#define MIN_DOT_PROD 50 /* min value of at->stereo_bond_z_prod[i] to define parity */

◆ MULT_STEREOBOND

#define MULT_STEREOBOND

Value:

0x08 /* multiplier for cumulene chain length

odd length => chiral, even length => stereogenic bond */

◆ NO_ISOLATED_NON_6RING_AROM_BOND

#define NO_ISOLATED_NON_6RING_AROM_BOND 0 /* for Yuri */

◆ NUM_CHEM_ELEMENTS

#define NUM_CHEM_ELEMENTS 127 /* well above number of known chem. elements */

◆ PARITY_CALCULATE

#define PARITY_CALCULATE ( X ) (AB_PARITY_CALC == PARITY_VAL(X))

◆ PARITY_ILL_DEF

#define PARITY_ILL_DEF ( X ) (AB_MIN_ILL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_ILL_DEFINED_PARITY)

◆ PARITY_KNOWN

#define PARITY_KNOWN ( X ) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY)

◆ PARITY_PART_DEF

#define PARITY_PART_DEF ( X ) (AB_MIN_PART_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_PART_DEFINED_PARITY)

◆ PARITY_VAL

#define PARITY_VAL ( X ) ((X) & BITS_PARITY)

◆ PARITY_WELL_DEF

#define PARITY_WELL_DEF ( X ) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY)

◆ SAVE_6_AROM_CENTERS

#define SAVE_6_AROM_CENTERS 0 /* for Yuri */

Typedef Documentation

◆ AT_ISO_SORT_KEY

typedef long AT_ISO_SORT_KEY

◆ AT_ISOTOPIC

typedef struct tagIsotopicAtom AT_ISOTOPIC

◆ AT_STEREO

typedef AT_NUMB AT_STEREO

◆ AT_STEREO_CARB

typedef struct tagStereoCarb AT_STEREO_CARB

◆ AT_STEREO_DBLE

typedef struct tagStereoDble AT_STEREO_DBLE

◆ sp_ATOM

typedef struct tagAtom sp_ATOM

Data Structures

Macros

Typedefs